Carbon-sink potential of continuous alfalfa agriculture lowered by short-term nitrous oxide emission events

Alfalfa is the most widely grown forage crop worldwide and is thought to be a significant carbon sink due to high productivity, extensive root systems, and nitrogen-fixation. However, these conditions may increase nitrous oxide (N2O) emissions thus lowering the climate change mitigation potential. We used a suite of long-term automated instrumentation and satellite imagery to quantify patterns and drivers of greenhouse gas fluxes in a continuous alfalfa agroecosystem in California. We show that this continuous alfalfa system was a large N2O source (624 ± 28 mg N2O m2 y−1), offsetting the ecosystem carbon (carbon dioxide (CO2) and methane (CH4)) sink by up to 14% annually. Short-term N2O emissions events (i.e., hot moments) accounted for ≤1% of measurements but up to 57% of annual emissions. Seasonal and daily trends in rainfall and irrigation were the primary drivers of hot moments of N2O emissions. Significant coherence between satellite-derived photosynthetic activity and N2O fluxes suggested plant activity was an important driver of background emissions. Combined data show annual N2O emissions can significantly lower the carbon-sink potential of continuous alfalfa agriculture.

Ln 549: Repository information needed (e.g. website link or citation). Figures 1,2,and 4 contain data that is too inter-connected and sometimes redundant to be stand-alone figures. It is not immediately clear to me why they are separate, so I suggest combining into one sevenpanel figure. Alternatively, I would suggest pulling soil NH4+ and NO3-data from Fig 4 and 2, respectively, into their own figure, since these were not sensor-based measurements and took place over a shorter time period, and combine all sensor-based measurements.    The potential offsetting of soil carbon sequestration through N2O emissions from an irrigated alfalfa crop is the focus of this study. Eddy covariance measurements were conducted over 4 years capturing several emission events (hot moments) associated with irrigation. The methodology is sound, results are clearly presented for the most part and the manuscript is well written. However, I have two main concerns: 1) the interpretation of the N2O flux results and its generalization to 'alfalfa agriculture'; 2) a lack of clear explanation of what the 'novel sensor suite' is exactly, and how it provided integrated information that improved our understanding of GHG fluxes.
I am providing detailed comments on each of these concerns below.
1) the interpretation of the N2O flux results and its generalization to 'alfalfa agriculture'; The hypothesis is "that elevated NO3 concentrations and irrigation during the growing season would stimulate hot moments of N2O emission, offsetting a significant portion of the net CO2-equivalent (CO2e) sink." Alfalfa is a perennial legume crop and hence nitrate levels would be expected to be minimized during the growing season in comparison to annual crops receiving N inputs in the form of manure or synthetic fertilizer such as corn or wheat. In fact, increased use of perennials is recognized as an N2O-mitigating practice.
I was at first surprised by the hypothesis statement, but results of high N2O emissions were corroborated with measurements, surely indicating elevated NO3 levels likely from soil organic matter mineralization. A closer look at the site's soil characteristics such as C levels indicates this may be an organic soil (or at least has very high levels of C), which are well known to have very high N2O emissions. In fact, Pärn et al. (2018) identify N rich organic soils under well-drained conditions as global N2O hot spots. Pärn et al. (2018) refer to a US-CA hot-spot based on a sampling site at Lat. 38.0169 N, W, close to the experimental site of 38.11ºN, 121.5ºW. Anthony and Silver (2021) did measure N2O fluxes with automated chambers at what appears to be an adjacent site to this study also identifying this area as a hot-spot of N2O fluxes (in this case the site had soil C values about 3x as reported here). However, in this manuscript the relatively high C levels of the site are not brought up as a potential major driver.
In addition, it appears that the Ryde soil series does have relatively low pH (not reported in manuscript). However, the role of soil organic matter and of the low pH in driving high soil N2O production is not considered in the interpretation of N2O flux results. Rather, the focus is on the role of alfalfa plants.
I think it is very difficult to separate the two effects (soil vs. plants) based on the set of measurements conducted, even though the authors collected a relatively long and complete time series of N2O fluxes. The main short-coming is the lack of a comparison (fallow field vs. alfalfa?, annual unfertilized crop vs. alfalfa?) that would allow for teasing out the main drivers. I expect a fallow or annual crop, irrigated field at this site would see even higher N2O fluxes than observed due to the high carbon and nitrogen substrates fueling denitrification and the acidic conditions favoring a higher N2O/N2 ratio. This means that alfalfa could actually be working to decrease emissions under these very favorable conditions for N2O production. Although measurements in  were made at a different sites (and different soils) in the same area, it would be interesting to compare these datasets.
I also miss an interpretation of the unique conditions of the experimental site vis-à-vis areas where alfalfa is grown in the US or the world. For example, the statement "Our results show that N2O emissions can significantly lower the C sink potential of this globally important crop" (L. 206) implies that experimental results could perhaps be applicable to other areas and any caveats are not identified. Instead, it is suggested that the high N2O fluxes are due to the intensive sampling (see L. 72 "Annual mean N2O fluxes were 624.4 ± 26.8 mg N2O m-2 yr-1 (Table 1, range: 247.0 ± 5.7 to 901.9 ± 74.5 mg N2O m-2 yr-1) and were significantly greater than other N2O flux estimates in alfalfa using less intensive periodic sampling (16-19)") and the unique soil conditions are not considered.
2) The lack of clear explanation of what the 'novel sensor suite' is exactly, and how it provided integrated information that improved our understanding of GHG fluxes.
Several times reference is made to a 'novel sensor suite'. For example, in the Abstract: "Using a novel suite of continuous soil sensing, eddy covariance, and satellite imagery we found that N2O emissions offset the ecosystem greenhouse gas sink by up to 14% annually" and L. 23 "Data from this novel sensor suite show that N2O emissions significantly lower the carbon-sink potential of alfalfa agriculture." However, the main finding of a 14% emission offset is based on the eddy covariance measurements alone. Although, EC measurements of N2O fluxes are not nearly as widespread as for CO2 and H2O, or even CH4, I would not classify the EC technique as novel. Similar high temporal resolution data as presented here can also be derived with automated chambers as Anthony and Silver (2020) have done for an adjacent site, but do not have the advantage of fluxes being spatially integrated over large areas like EC has.
The continuous soil sensing was used to provide some explanation for the flux drivers as is often done in N2O studies. The satellite imagery was used to find "Significant coherence between satellite derived vegetation growth and N2O fluxes suggested that plant activity was an important driver of background emissions" (Abstract) and "Background fluxes varied with moisture, temperature, and NIRv, an index of GPP. Lagged relationships between NIRv, CO2, and N2O fluxes suggested that plant inputs were likely an important driver of soil CO2 fluxes and background N2O emissions." (L. 204). I consider the latter conclusion a bit tenuous since plant inputs (presumably substrate for nitrifiers and denitrifiers) were not specifically quantified and compared to soil substrate supply. In addition, this relationship was only

RESPONSE TO REFEREES
Reviewer #1 (Remarks to the Author): Overview and general recommendations: The submitted manuscript quantifies the contributions of soil nitrous oxide (N2O) fluxes, and particularly from hot moments, to CO2e balance for alfalfa agroecosystems. Using a novel dataset of multi-year, continuous, high-resolution chamber flux measurements coupled with belowground sensors and periodic soil sampling, the study highlights novel findings that hot moments of N2O, although appearing in less than 2% of measurements, accounted for almost half of annual N2O emissions and substantially offset the ecosystem carbon sink previously estimated for alfalfa. Consistent with recent literature, most hot moments occurred during soil re-wetting events, when anaerobic microsites may be generated, and were additionally modulated by temperature and by crop activities. Data collection, processing, and analytical methods are described well and are consistent with common practices of soil and ecosystem scientists. My primary concern regarding the quality of the current manuscript lies in the contextualization of results to the broad readership of Nature Communications, and I believe this concern can be alleviated by addressing my comments below. I am not completely convinced of the relevance of the CH4 measurements to the study and suggest a couple of different ways to integrate this dataset better with CO2 and N2O. I am also concerned that the broader impacts of this work to agroecosystems and/or to drylands are lost due to the focus on one particular crop species, albeit one that is grown widely. Finally, although the results are presented well, they don't fully match with the introductory material and hypothesis provided; I suggest expanding your hypothesis to include other drivers of N2O and CO2e that you measure and that are more holistic to addressing N2O contributions to alfalfa C balance. I am confident that addressing these concerns will increase the quality of the manuscript and will accelerate its timeline to publication.
We thank the reviewer for their comments. We appreciate the suggestions to broaden the contextualization and better integrate the CO2 and CH4 data and have made the detailed changes suggested (outlined below). We have also expanded the first hypothesis as suggested and added a second hypothesis that states, "We also hypothesized that background patterns in N2O emissions would follow patterns in plant activity indicative of potential changes in C or substrate availability." Line numbers cited below represent numbers with track changes on.
Specific comments: Abstract: Since considerable text and one figure are dedicated to describing patterns and mechanisms of diel and seasonal fluxes of N2O, I anticipated those to be reported somewhere in the abstract. I suggest a few words or short sentence to describe main findings.
Introduction: Given the title and focus of the paper, the connections between your trace gases of interest needs more explicit description. For example, CO2 also produces respiration pulses during irrigation but at different timing and using different metabolic mechanisms, but ecosystem CO2 fluxes are not described in the introduction. I suggest to more fully describe CO2 fluxes to complement the description of CH4 and round out the background of all three gases of interest, or to instead to describe CH4 and CO2 together as having hot moments of carbon or CO2e exchange that may be enhanced by N2O flux and offset the non-hot-moment C sink. For a further biogeochemical perspective, there is considerable literature showing interactions between methanotrophy and N2O production that could support the inclusion of CH4 and N2O data together, and why a soil CH4 sink could lead to an N2O source. This may be useful to return to in your discussion as well.
Additional text regarding CO2 and CH4 fluxes was added in the introduction (L61-L77) and discussion (L213-216). We also now mention that eddy covariance studies suggest that alfalfa agroecosystems are net C sinks even with potential pulses of CO 2 and CH 4 emissions, but data on continuous N2O emissions are lacking.
Results/Discussion: Since you described a hypothesis in your introduction, I would like to see a conclusion in the last paragraph (or elsewhere if more appropriate) about whether that hypothesis was supported. You address pieces of it throughout but I don't see them integrated explicitly. I also suggest moving your supplemental GWP results to the main text as I find those particularly compelling.
We have added a conclusions section and made the suggested changes which we agree really help highlight the findings and significance. (L248-254). We also integrated the supplemental GWP results to the main text as suggested (L110-117).
Ln 61: A word is missing in this sentence: "…patterns and associated [mechanisms maybe?] of CO2…" We have added the word "controls".
Ln 66-68: I was not expecting this hypothesis given the diversity of measurements reported here; particularly, I would have expected NH4+ and O2 to be included as hypothesized drivers of N2O emission since they were described earlier in the introduction. Is there a reason these were not included but NO3-was? Temperature/climatic drivers of emissions are not really introduced in the introduction and do not appear in hypotheses but are contained in multiple figures and results; consider including them here and in the intro at large.

We expanded the hypotheses as suggested and added some text to the introduction to better justify the hypotheses and provide background for the measurements made to test the hypotheses.
Ln 103: A word is missing in this sentence: "…from greater [?] and C and substrate availability…"

This has been changed to "greater C and N substrate availability" (L140)
Ln 184: I suggest including this as a new subsection titled "Aboveground C dynamics" or "Alfalfa C sequestration" as this paragraph includes alfalfa C sink and eddy covariance data rather than just soil CO2 emissions. Or, make the heading of Ln 173 more inclusive as "Agroecosystem CO2 balance" or similar to capture both above and belowground fluxes.
We have changed the heading to "Agroecosystem CO2 balance" (L218) Ln 200: I suggest including this as a new subsection titled "synthesis" or "conclusions" as it integrates all data rather than just CO2 fluxes.
We added a conclusions section as suggested.
Ln 216: How much land area is used for alfalfa? This information, with included citation, would be useful for upscaling.

We clarify that alfalfa and corn are the dominant agricultural land uses in the region, with alfalfa representing 20% of agricultural land area in the Sacramento-San Joaquin Delta (The Delta Protection Commission, 2020) and the largest crop by area in California and the (Putnam et al. 2007). Nearly 100% of alfalfa in California is irrigated (Putnam et al. 2007). (L270-L274).
Ln 341: Suggest to replace "gappy" with "discontinuous" or "noncontinuous." We have replaced "gappy time series" with "time series with missing observations" (L400).
Repository information has been added as Source Data and as: https://datadryad.org/stash/share/igfrCACBTOMTNEi8KsL3auVLnSqKiN51WFRUlFf04Ds. Figures 1,2,and 4 contain data that is too inter-connected and sometimes redundant to be stand-alone figures. It is not immediately clear to me why they are separate, so I suggest combining into one seven-panel figure. Alternatively, I would suggest pulling soil NH4+ and NO3-data from Fig 4 and 2, respectively, into their own figure, since these were not sensorbased measurements and took place over a shorter time period, and combine all sensor-based measurements.  We have addressed the suggestions above and combined and rearranged the figures: Figure 1 contains N2O, CH4, and CO2 fluxes with soil moisture, temperature, O2, and NIRv. Figure 3 now contains NO3, NH4, and soil pH observations. Table 2: Do the + signs in hot moment % of total flux add additional information? To me, a percentage alone seems sufficient.
We have removed the + signs from Table 2.

Reviewer #2 (Remarks to the Author):
Review of 'Hot moments of nitrous oxide emissions lower the carbon-sink potential of alfalfa Agriculture' by Anthony et al. The potential offsetting of soil carbon sequestration through N2O emissions from an irrigated alfalfa crop is the focus of this study. Eddy covariance measurements were conducted over 4 years capturing several emission events (hot moments) associated with irrigation. The methodology is sound, results are clearly presented for the most part and the manuscript is well written. However, I have two main concerns: 1) the interpretation of the N2O flux results and its generalization to 'alfalfa agriculture'; 2) a lack of clear explanation of what the 'novel sensor suite' is exactly, and how it provided integrated information that improved our understanding of GHG fluxes.
I am providing detailed comments on each of these concerns below.
We thank the reviewer for their comments and address them specifically below.
1) the interpretation of the N2O flux results and its generalization to 'alfalfa agriculture'; The hypothesis is "that elevated NO3 concentrations and irrigation during the growing season would stimulate hot moments of N2O emission, offsetting a significant portion of the net CO2equivalent (CO2e) sink." Alfalfa is a perennial legume crop and hence nitrate levels would be expected to be minimized during the growing season in comparison to annual crops receiving N inputs in the form of manure or synthetic fertilizer such as corn or wheat. In fact, increased use of perennials is recognized as an N2O-mitigating practice.
We agree that the assumption is often that an N-fixing perennial crop does not experience hot moments of NO3availability or N2O emissions. However, the high-resolution measurements we were able to achieve showed that NO3concentrations were not uniformly low, and this together with periods of high soil moisture led to hot moments of N2O emissions. We have added text in the introduction to better summarize these issues (L88-95) and expanded the hypotheses and explanations as suggested by reviewer one.
I was at first surprised by the hypothesis statement, but results of high N2O emissions were corroborated with measurements, surely indicating elevated NO3 levels likely from soil organic matter mineralization. A closer look at the site's soil characteristics such as C levels indicates this may be an organic soil (or at least has very high levels of C), which are well known to have very high N2O emissions. In fact, Pärn et al. (2018) identify N rich organic soils under welldrained conditions as global N2O hot spots.  (2021) did measure N2O fluxes with automated chambers at what appears to be an adjacent site to this study also identifying this area as a hot-spot of N2O fluxes (in this case the site had soil C values about 3x as reported here). However, in this manuscript the relatively high C levels of the site are not brought up as a potential major driver.
We now mention soil organic matter can be a potential driver of greenhouse gas emissions but note that this site has lower soil C and N than others in the regions (L145-146,L220). The three sites in the Sacramento-San Joaquin Delta described above have widely ranging surface soil C concentrations ( In addition, it appears that the Ryde soil series does have relatively low pH (not reported in manuscript). However, the role of soil organic matter and of the low pH in driving high soil N2O production is not considered in the interpretation of N2O flux results. Rather, the focus is on the role of alfalfa plants.
We agree the low pH can be a contributor to the magnitude of hot moments. Soil pH was measured weekly alongside soil mineral N values (added as Figure 2c) and relevant text has been added clarifying the effects of an acidic soil pH (L53-55, L143-146).
I think it is very difficult to separate the two effects (soil vs. plants) based on the set of measurements conducted, even though the authors collected a relatively long and complete time series of N2O fluxes. The main short-coming is the lack of a comparison (fallow field vs. alfalfa?, annual unfertilized crop vs. alfalfa?) that would allow for teasing out the main drivers. I expect a fallow or annual crop, irrigated field at this site would see even higher N2O fluxes than observed due to the high carbon and nitrogen substrates fueling denitrification and the acidic conditions favoring a higher N2O/N2 ratio. This means that alfalfa could actually be working to decrease emissions under these very favorable conditions for N2O production. Although measurements in  were made at a different sites (and different soils) in the same area, it would be interesting to compare these datasets.
We understand the reviewer's comments, but respectively disagree that a comparison to other crops or a fallowed field is needed to determine the main drivers of N2O in this context.

Here we used wavelet coherence to parse relationships among variables measured. It is a useful tool for studying fluctuations across data-rich time series and can be used to determine significance and elucidate scale-emergent interactions between variables (Chamberlain et al. 2018, Rodríguez-Murillo and Filella, 2020, Sturtevant et al., 2016). A more detailed description of wavelet coherence has been added to the text (L389-L392). Comparisons with a fallowed field or irrigated annual crop, while interesting, would be asking a different question than the one addressed here. Fallow and annual cropping are different management activities that change multiple environmental and biogeochemical conditions when compared to alfalfa agriculture. Annual cropping is conducted on different soils. Thus, we don't feel that a comparison with corn cropping would help us determine the impacts of alfalfa on N2O
emissions. In this instance we explored the potential role of plant productivity in greenhouse gas fluxes when compared with other drivers occurring under the same environmental conditions. We now clarify and qualify this result more carefully to address the reviewer's concerns. We included text stating that these degraded peatland soils that have lost a significant proportion of their initial organic matter and contain significantly higher mineral content than intact or nutrient-rich peatland soils by citing Anthony and Silver (2020). We have added text throughout to clarify these issues.

I also miss an interpretation of the unique conditions of the experimental site vis-à-vis areas
where alfalfa is grown in the US or the world. For example, the statement "Our results show that N2O emissions can significantly lower the C sink potential of this globally important crop" (L. 206) implies that experimental results could perhaps be applicable to other areas and any caveats are not identified. Instead, it is suggested that the high N2O fluxes are due to the intensive sampling (see L. 72 "Annual mean N2O fluxes were 624.4 ± 26.8 mg N2O m-2 yr-1 ( Table 1, range: 247.0 ± 5.7 to 901.9 ± 74.5 mg N2O m-2 yr-1) and were significantly greater than other N2O flux estimates in alfalfa using less intensive periodic sampling (16-19)") and the unique soil conditions are not considered.
We agree that more information regarding our site in relation to alfalfa agriculture is warranted and has been included (L31-L33, L50-L51, L267-L274). These are highly degraded peatland soils that have lost a significant proportion of their initial organic matter content and contains significantly higher mineral concentrations than intact or nutrient-rich peatland

soils (Anthony and Silver 2020). We clarify that the management of the site is representative of alfalfa agriculture across the region as nearly 100% of alfalfa in California in irrigated, and approximately 82% is similarly flood irrigated (Long et al. 2022). We have added text (L272-L273) comparing our site to general irrigation management and soil types, adding caveats regarding soil pH (L143-L145, L170-L172).
In L121-L125 we also clarify why we believe intensive sampling is important. Not missing these hot moments (which represent <1% of observations but an average of 44% of emissions) more accurately captures short-term hot moment N2O emissions where noncontinuous sampling methods can miss rare high flux events.
2) The lack of clear explanation of what the 'novel sensor suite' is exactly, and how it provided integrated information that improved our understanding of GHG fluxes.
Several times reference is made to a 'novel sensor suite'. For example, in the Abstract: "Using a novel suite of continuous soil sensing, eddy covariance, and satellite imagery we found that N2O emissions offset the ecosystem greenhouse gas sink by up to 14% annually" and L. 23 "Data from this novel sensor suite show that N2O emissions significantly lower the carbon-sink potential of alfalfa agriculture." However, the main finding of a 14% emission offset is based on the eddy covariance measurements alone. Although, EC measurements of N2O fluxes are not nearly as widespread as for CO2 and H2O, or even CH4, I would not classify the EC technique as novel. Similar high temporal resolution data as presented here can also be derived with automated chambers as  have done for an adjacent site, but do not have the advantage of fluxes being spatially integrated over large areas like EC has.
We agree clarification in the novel sensor suite is needed and believe this caused some of the misunderstanding described here. We have added text clarifying that this study used "a novel suite of automated flux chambers (to quantify continuous CO2, N2O and CH4 fluxes) combined with continuous soil sensing, eddy covariance (to quantify net ecosystem CO2 exchange) , and satellite imagery" in the abstract (L18-19) and introduction (L81-L83). We do not suggest that EC, even with N2O, is novel, rather the novelty is provided by the combination of long-term automated chamber, continuous soil sensing, satellite imagery, and eddy covariance observations. The continuous soil sensing was used to provide some explanation for the flux drivers as is often done in N2O studies. The satellite imagery was used to find "Significant coherence between satellite derived vegetation growth and N2O fluxes suggested that plant activity was an important driver of background emissions" (Abstract) and "Background fluxes varied with moisture, temperature, and NIRv, an index of GPP. Lagged relationships between NIRv, CO2, and N2O fluxes suggested that plant inputs were likely an important driver of soil CO2 fluxes and background N2O emissions." (L. 204). I consider the latter conclusion a bit tenuous since plant inputs (presumably substrate for nitrifiers and denitrifiers) were not specifically quantified and compared to soil substrate supply. In addition, this relationship was only found for background N2O emissions while as described in this manuscript, hot moments are the main overall drivers of N2O emissions.
Here we used wavelet coherence to compare variables across time series and infer relationships among variables. We have added text in the introduction regarding substrate availability (L65-71) and clarified that our plant activity metric (NIRv) specifically represents photosynthetic activity (L24-25, L82-L83, L277-282). NIRv is an accurate method to determine canopy photosynthesis , and photosynthesis is the primary source of C inputs into terrestrial ecosystems. Root exudates are well-known labile soil C sources that can prime microbial activity (Panchal et al. 2022), with up to 20% of C fixed by photosynthesis released by root exudation (Guyonnet et al. 2018, Haichar et al., 2008). Thus, the relationships with plant photosynthetic activity are an index of plant C inputs and activity (L65-L70, L280-L282). We have clarified that the observed lagged relationships may represent delays between photosynthetic C uptake and root exudation processes (L242-244). We have also soften the language to suggest that these patterns are one possible driver of the background patterns observed.

Hot moments of emissions appear to have been driven by O2, and moisture at daily scales, and that lagged (weekly to monthly) relationships between NIRv and N2O fluxes suggests plant inputs were likely an important driver background N2O emissions (L176-L187).
The submitted manuscript quantifies the contributions of soil nitrous oxide (N2O) fluxes, and particularly from hot moments, to CO2e balance for alfalfa agroecosystems. Using a novel dataset of multi-year, continuous, high-resolution chamber flux measurements coupled with belowground sensors and periodic soil sampling, the study highlights novel findings that hot moments of N2O, although appearing in less than 2% of measurements, accounted for almost half of annual N2O emissions and substantially offset the ecosystem carbon sink previously estimated for alfalfa. Consistent with recent literature, most hot moments occurred during soil re-wetting events, when anaerobic microsites may be generated, and were additionally modulated by temperature and by crop activities. Data collection, processing, and analytical methods are described well and are consistent with common practices of soil and ecosystem scientists.
After reading responses to reviewers and the revised manuscript, I am pleased with the changes the authors have made and I think revisions have made clear the importance and nuance of these results. I have a few comments regarding minor detail changes, but I think generally this manuscript is ready to move forward to publication. Great work! Specific comments: Abstract: I think somewhere in here you need to mention CO2 and CH4 as measured carbon fluxes since those are a big chunk of your results and you spend a lot of text describing them. The least invasive way to include them might be in Ln 18-19: "…offsetting the ecosystem carbon (CO2 and CH4) sink by …". Or something more elegant. I think it's important to specify somehow that you looked at CH4 in addition to CO2, since readers may assume only CO2 was measured here.
Ln 59-60: This citation does not have a matching reference in References section and is different annotation than other citations.
Ln 163-165: I'm getting confused by the wording here; can you write this sentence more simply? Is it that lower GPP tended to match low background N2O?
Reviewer #2 (Remarks to the Author): Thank you for addressing many of my comments and clarifying certain issues. I still have major concerns as to how the results are interpreted and conveyed to readers. The main take away message is that 'alfalfa agriculture' emits significant amounts of N2O, enough to offset the C-sink potential. The high overall annual N2O emissions (=4 kg N/ha/yr with range of 1.6 to 5.7) occur over somewhat frequent and short periods of time associated with irrigation and driven by high N levels released by the high SOM content at the measurement site (Hot moments). I commented on the high SOM in my previous review and although the reply was that the site is on highly degraded peatland soil, the SOM content is still quite high compared to regular mineral soils. This means that the results obtained here can not be easily generalized to 'alfalfa agriculture' as the authors have done in Abstract and Conclusions. A much more nuanced interpretation of the measurements is needed. In fact, N2O emissions are notoriously variable with soil type, management and weather events and generalizing results from one site is not possible. For example, Tenuta et al. (2019) using a micromet approach show that including perennial crops such as alfalfa in crop rotations leads to much lower N2O emissions that annual crops, in contrast to this study.
In addition, the authors argue the large N2O emissions measured in this study are due to the measurement method used. For example in L. 89-91 "Annual mean N2O fluxes were 624.4 ± 26.8 mg …… and were significantly greater than other N2O flux estimates in alfalfa using less intensive periodic sampling30-33.". While I strongly agree that more continuous measurements as provided by micromet methods are sorely needed and provide a much better flux time series, I think a more nuanced interpretation is also needed here. Firstly, the citations given here are not appropriate to support the argument made.
Ref 30: reports on emissions that are of a similar order of magnitude (2.3 and 5.7 kg N/ha/yr) with measurements made using static chambers; Ref 32: is a micromet study with frequent observations; Ref 33: reports on canola and wheat N2O emissions following alfalfa termination for a semi-arid region.
Secondly, as demonstrated by Ref30 the high emission peaks could be captured with other methods in an irrigated alfalfa system since they are quite predictable and timed with the irrigation. In fact, there may be an issue with overestimation given that chamber studies will typically target high emission events and then interpolate between these weekly data points to obtain annual emissions.

Responses by the authors are in bold. Corresponding line numbers refer to line numbers with track changes on.
Reviewer #1 (Remarks to the Author): Overview and general recommendations: The submitted manuscript quantifies the contributions of soil nitrous oxide (N2O) fluxes, and particularly from hot moments, to CO2e balance for alfalfa agroecosystems. Using a novel dataset of multi-year, continuous, high-resolution chamber flux measurements coupled with belowground sensors and periodic soil sampling, the study highlights novel findings that hot moments of N2O, although appearing in less than 2% of measurements, accounted for almost half of annual N2O emissions and substantially offset the ecosystem carbon sink previously estimated for alfalfa. Consistent with recent literature, most hot moments occurred during soil re-wetting events, when anaerobic microsites may be generated, and were additionally modulated by temperature and by crop activities. Data collection, processing, and analytical methods are described well and are consistent with common practices of soil and ecosystem scientists. After reading responses to reviewers and the revised manuscript, I am pleased with the changes the authors have made and I think revisions have made clear the importance and nuance of these results. I have a few comments regarding minor detail changes, but I think generally this manuscript is ready to move forward to publication. Great work! We thank the reviewer for their comments.
Specific comments: Abstract: I think somewhere in here you need to mention CO2 and CH4 as measured carbon fluxes since those are a big chunk of your results and you spend a lot of text describing them. The least invasive way to include them might be in Ln 18-19: "…offsetting the ecosystem carbon (CO2 and CH4) sink by …". Or something more elegant. I think it's important to specify somehow that you looked at CH4 in addition to CO2, since readers may assume only CO2 was measured here.
We removed this sentence as it is repetitive of third sentence of the paragraph, which is cited.
Ln 59-60: This citation does not have a matching reference in References section and is different annotation than other citations.

This has been corrected.
Ln 163-165: I'm getting confused by the wording here; can you write this sentence more simply? Is it that lower GPP tended to match low background N2O?
The text (L171-176) has been changed to: "Increases in background (low-level) N2O emissions were positively correlated with periods of high gross primary productivity (GPP), measured with satellite observations of near infrared reflectance of vegetation(NIRv) 1 ." Reviewer #2 (Remarks to the Author): Thank you for addressing many of my comments and clarifying certain issues. I still have major concerns as to how the results are interpreted and conveyed to readers. The main take away message is that 'alfalfa agriculture' emits significant amounts of N2O, enough to offset the Csink potential. The high overall annual N2O emissions (=4 kg N/ha/yr with range of 1.6 to 5.7) occur over somewhat frequent and short periods of time associated with irrigation and driven by high N levels released by the high SOM content at the measurement site (Hot moments). I commented on the high SOM in my previous review and although the reply was that the site is on highly degraded peatland soil, the SOM content is still quite high compared to regular mineral soils. This means that the results obtained here can not be easily generalized to 'alfalfa agriculture' as the authors have done in Abstract and Conclusions. A much more nuanced interpretation of the measurements is needed. In fact, N2O emissions are notoriously variable with soil type, management and weather events and generalizing results from one site is not possible. For example, Tenuta et al. (2019) using a micromet approach show that including perennial crops such as alfalfa in crop rotations leads to much lower N2O emissions that annual crops, in contrast to this study.
We thank the reviewer for their thorough review and careful reading of the paper. We now better understand the reviewers concerns regarding SOM stocks described above and the need to include a more nuanced interpretation of our results. We have included additional text regarding this in L139-142.
With regard to generalizing these results to continuous alfalfa agriculture, we note that apart from this study, combined multi-year continuous flux measurements of CO2, CH4, and N2O in continuous flood-irrigated alfalfa are essentially non-existent, even though this is the predominant practice for alfalfa in regions like the Western United States 2 (Text added in L93-96). Understanding the drivers of interannual variability, and accurately quantifying differences in emissions with stand age 3 are needed to upscale emissions, particularly for N2O which we show is inherently variable. To address the reviewers concerns we clarify that continuous measurements are needed to assess greenhouse gas emissions and the net C balance of continuous alfalfa ecosystems, as these are likely to differ from other agricultural activities including those that incorporate alfalfa in short-term rotations (L37-40).
The reviewer cites Tenuta et al. (2019) as an example of alfalfa agriculture leading to lower N2O emissions than annual cropping. As mentioned previously, our goal here was not to compare alfalfa with annual cropping but to quantify continuous fluxes from multi-year continuous alfalfa agriculture, an important crop globally. This is fundamentally different from the mixed cropping system described in Tenuta et al. 2019. Regardless we have added some text to qualify our results stating, "This suggests net N2O emissions from irrigated alfalfa may not always be reduced relative to other agricultural ecosystems receiving inorganic N inputs, particularly on relatively C-rich soils". (L101-103).
In addition, the authors argue the large N2O emissions measured in this study are due to the measurement method used. For example in L. 89-91 "Annual mean N2O fluxes were 624.4 ± 26.8 mg …… and were significantly greater than other N2O flux estimates in alfalfa using less intensive periodic sampling 30-33.". While I strongly agree that more continuous measurements as provided by micromet methods are sorely needed and provide a much better flux time series, I think a more nuanced interpretation is also needed here. Firstly, the citations given here are not appropriate to support the argument made. Ref 30: reports on emissions that are of a similar order of magnitude (2.3 and 5.7 kg N/ha/yr) with measurements made using static chambers; Ref 32: is a micromet study with frequent observations; Ref 33: reports on canola and wheat N2O emissions following alfalfa termination for a semi-arid region.
We have changed and added nuance to the corresponding text (L92-96) and have added the following to the conclusions (L255-258): "This combination of automated chambers, eddy covariance, soil sensing, and satellite imagery is the most comprehensive dataset of multiyear annual budgets from continuous alfalfa agriculture to date, allowing us to determine the importance of both hot and non-hot moment emissions on total N2O budgets and explore scale-emergent drivers of N2O emissions." Long-term (> 2 years) continuous flux measurements, specifically of continuous alfalfa, are essentially non-existent. However, the above references, with the addition of Tanuta et al. 2019 4 (although a grass/alfalfa mixture), and two additional references 5 , were some of the only potentially comparable annual estimates. We have removed the Malhi 2010 6 reference and have clarified that some of these estimates are not from continuous alfalfa ecosystems (L94-96).
Secondly, as demonstrated by Ref30 the high emission peaks could be captured with other methods in an irrigated alfalfa system since they are quite predictable and timed with the irrigation. In fact, there may be an issue with overestimation given that chamber studies will typically target high emission events and then interpolate between these weekly data points to obtain annual emissions.
We agree that capturing high emissions events are important for calculating total budgets, and that our data show that irrigated fields may have more predictable hot moment fluxes than other agroecosystems. In L115-119 we state that continuous measurements ensure all hot moments are captured as well as non-hot moment emissions that accounted for ~50% of the flux. We do not think that the chamber-based approach here was likely to overestimate fluxes because it was continuous. Micromet approaches cover a wider land area, but the comparatively high detection limit of most tower-based micromet N2O measurement approaches (for example see Tenuta et al. 2016 7 , 2019 4 ) could potentially lead to underestimated fluxes.
The final point of concern (which I missed in my first review) is the lack of consideration in C removal in harvest when determining if the field is a carbon sink. In fact, some information about forage yields and C content should be included.